This study used panel data selected from 1838 county-level administrative regions for the period 2003–2018 on the opening of high-speed railway in China. Using the  (DID) method, the impact of transportation infrastructure construction on population agglomeration in different counties was studied by utilizing the exogenous impact of high-speed railway opening. Baseline regression results and robustness tests indicated that the opening of high-speed railways in the selected counties has significantly promoted population agglomeration compared to counties without high-speed railways. This result further proves that transportation infrastructure construction can directly improve a county's population agglomeration level, while labour mobility plays an effective intermediary role in the agglomeration effect. Also, the county population agglomeration effect produced by the construction of transportation infrastructure has a significant administrative division heterogeneity and geographical location heterogeneity. Additionally, due to the “siphon effect” and “trickle-down effect” of the central city, counties within different geographic distance circles exhibit different agglomeration characteristics after the construction of transportation infrastructure. Generally, with an increase in the distance from the central city, the population agglomeration effect shows an “inverted U-shaped” change trend where the threshold for high-speed rail is 200 km. This study provides theoretical support and a practical basis for railway layout, population element allocation, and coordinated regional development.